Coat a large saucepan generously with extra virgin olive oil. Add the onions and bring to a medium high heat. Season generously with salt and add the crushed red pepper. Saute until the onions are translucent and very aromatic, about 7 to 8 minutes. Add the garlic and saute for another minute. Add the tomatoes. Fill the tomato can with water and add to the pan. Season with salt and cook over medium heat for about 10 to 15 minutes or until the water has reduced. Add the squash, stock, and bay leaf. Taste for seasoning and season with salt if needed. Cook until the squash is cooked through and most of the liquid has absorbed, about 20 to 30 minutes.
Bring a pan of well-salted water to a boil. Add the fregula and cook until it is cooked through but still al dente, about 8 to 10 minutes. Strain and add to the pot with tomatoes and squash. Stir to incorporate. Add more stock or water if the mixture is dry and cook longer if it is too soupy. When done it should have a stew-like consistency. Stir in the chives. This will be really good today but even better tomorrow!
*Fregula, a small round semolina pasta from Sardinia can be found in specialty food stores.